Distributions of phytoplankton density and their relationships to physicochemical variables were investigated using multivariate analyses, based on data collected every two months from a tropical, inland, freshwater estuary in southern Thailand between June 2005 and December 2007. Results indicated 74 genera of phytoplankton in the samples. More than 75% of the genera were diatoms (30 genera; 40.5%) and chlorophytes (29 genera; 39.2%), and 20% were cyanobacteria (6 genera; 8.1%) and dinoflagellates (6 genera; 8.1%). Variations in phytoplankton density largely resulted from salinity and turbidity, which varied seasonally and geographically. Chlorophytes, cyanobacteria, and euglenophytes were the most common groups in the turbid freshwater habitat, whereas diatoms and dinoflagellates dominated along the salinity gradient of the clear estuarine environment. Our results suggest that the Na Thap River has been regulated mainly by the natural phenomena of marine and riverine influences, even though the river is situated on agricultural, aquacultural, and industrial land. Continued observations of phytoplankton density and composition are needed, emphasizing any unusual increases in density and/or the unexpected presence of harmful species. The long-term trends of phytoplankton provide an indication of the change in the trophic status of the basin, as well as a foundation for further studies of the distributions of upper-level aquatic species in freshwater estuarine ecosystems.